Detect enhancer-promoter interactions and relate them to the dynamics of the chromatin fibre in live mammalian cells — Simultaneously detect transcription from the promoter and understand if, and to what extent, temporal variability in RNA production is the result of stochastic interactions with enhancers.
Generation of cell lines that allow the direct visualization of enhancer and promoter DNA using the targeted insertion of arrays of ectopic transcription factor binding sites (e.g. Tet operators or Gal4-UAS sites), bound by the corresponding DNA-binding proteins fused to green and red fluorescent proteins. Simultaneous visualization of several locations along the chromatin fiber between the enhancer and the promoter, using operator arrays inserted at regularly spaced locations between the enhancer and the promoter. Visualization of transcription from the promoter in living cells using MS2 stem-loop repeats. Cell lines will be characterized using high-resolution Hi-C. Live-cell imaging will be performed using wide-field and live STED microscopy.
Enhancers are thought to act on the genes that they control by physically looping on their promoter regions. However, it is unclear how dynamic these interactions are, and whether their dynamics is related to the RNA stochastic production from the promoter, which is commonly observed at most mammalian genes. This question will be addressed by visualising the spatial position of an enhancer and its target promoter in the nucleus, and the conformation of the chromatin fiber in the intervening region, together with RNA transcription from the promoter in live single mammalian cells. Quantitative data analysis and biophysical modelling will allow understanding if and to what extent enhancer-promoter contacts are causal to RNA production.
CNRS, France (3-6 months):
Perform live-cell STED microscopy and Hi-C.
CRG (P1b), Marc A. Marti-Renom (3 months):
Statistical analysis of datasets.
BYFACILITY, Spain (2 weeks):
Learning how to communicate complex information.
Enrolment in doctoral programs
Enrolment in FMI International PhD Program.
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